Here is something I wrote on this subject for people with fish-only tanks. It probably does not directly answer your question, but does provide more info to consider when you are deciding what to do.
If you want to keep that gravel, but improve conditions in the tank, I would start vacuuming it a little bit at a time, until (perhaps a couple of months from now) it is clean.

OLD TANK SYNDROME
Aquariums with less than optimum water changes will accumulate toxins that can poison the fish, shrimp, snails and plants. As nitrate climbs and the decomposing bacteria use up the minerals in the tank the pH can drop, to 6.0 and lower. Nitrospira bacteria (the actual nitrifying bacteria) do not do well at lower pH and may be dead. Ammonia climbs, pH drops, nitrate may be very high. The GH may be quite high if the tank has just been topped off using tap water.
The fish might have adapted to the high nitrate. Those that could not adapt have died. If you try adding new fish, they die. The low pH is keeping the ammonia in the NH4+ form, which is less toxic Any water changes create changes in the GH, KH and pH levels and the fish become sick or die.

This tank is suffering from Old Tank Syndrome. The best, safest cure is a long, slow change back to optimum conditions. The fish have been living like this long enough to adapt to the low GH, KH and pH as well as the high nitrate. An instant change back to 'perfect' would be too much for them.

Here is what I would do: (and why)

FIRST WEEK:

1) 10% daily or even twice daily water changes. Use a dechlorinator that locks up ammonia, nitrite and nitrate. Prime, Amquel Plus... (Any larger water change creates too big a water chemistry change)

2) Zeolite in the filters. Get 3 bags: every day swap out one bag and rejuvenate it overnight in salty water, then soak in fresh water (RO or Distilled is best) You will always have 2 bags in the tank, and one in rejuvenation. (Zeolite removes ammonia, but gets filled up. It is cheapest to buy a large jar of it and cut up some nylon stockings as bags.)

3) If there is over 1.5 watts of light add all the plants you can. Fast growing stuff like Anacharis is best. (Plants are the fastest ammonia removers. But under 1.5 watts they are more likely to rot than to help. If fish eat them, not to worry, just feed the fish less. Plants are low nitrogen compared to high protein fish food, thus contributing less ammonia waste to the problem)

4) Deep and thorough gravel vac as much as you can this week. (Decomposing gunk is lowering the pH and contributing to ammonia problem) 10% water change does not allow for much gravel vacuuming in any one session, but you can get over the whole tank bottom at least once this week.

5) Order Nitrospiros species of nitrifying bacteria. Microbe Lift’s Nite Out II, Tetra Safe Start and Dr. Tim’s One and Only are good. Do not waste your money on any other source of ‘bacteria in a bottle’. Wrong ingredients. Other sources of ntrifying bacteria include other healthy, cycled tanks. You could add some floss or sponge filter media from a healthy tank to this ailing tank, but the bacteria will not grow very well in such low pH. I would not add it this week. Do not take so much filter media from the established, healthy tank that it gets into trouble. These bacteria will not do very well when the pH is too low, but as soon as the pH has climbed to 6.5, add whatever source of bacteria you can to boost the population in the tank.

6) Feed less. Half what was fed before. Feed low protein foods if the fish can handle them. (This is the Garbage In = Garbage Out principle. Less GI = less GO.)

7) Clean the filter in water removed from the tank. Tap water with chloramines or chlorine can kill whatever nitrifying bacteria may be alive.

By the end of the first week the ammonia will be significantly lower, the pH slightly higher, nitrite might be showing and nitrate might still be very high. Gravel is much cleaner. O2 levels are rising, benefiting fish and nitrifying bacteria. If the tests show nitrite, add sodium chloride (salt) @ 1 teaspoon per 20 gallons of water. Add this much whenever you do a water change based on the amount of the water change. If you do a 5 gallon water change add .25 teaspoon to the new water. Keep this up until the nitrite level consistently reads 0 ppm.

SECOND WEEK

1) Do daily 20% water changes, and deep gravel vacs. Also, clean the filter. (The larger water changes are going to be altering the pH a bit more, but are removing a lot more nitrate. As the nitrifying bacteria get going again removing nitrate is very important.)

2) Add nitrifying bacteria. If you use a bottled product then no more gravel vacs the rest of the week, and no water changes for a couple of days. Do not clean any filter for a week. (Allow the bacteria to settle in the filters and gravel without removing it or knocking it off the gravel or filter media.) If you were able to get cycled media from a healthy tank then keep up the water changes and gravel vacs.

3) Continue swapping out the zeolite bags, but if the ammonia tests show that the ammonia is a lot lower, just swap out one bag every other day. (The nitrifying bacteria need ammonia to eat. By removing it with zeolite you are starving the bacteria. It takes several days for the bacteria to settle in and really get going on the ammonia, though, so keep the zeolite going this week. Might still need daily replacement)

4) Continue feeding the fish significantly less food. If they will eat vegetables or plants this is better.

After the second week I will expect the ammonia to be gone or almost gone. The nitrifying bacteria might be having a hard time. Be patient. It will get going soon. The pH may not be the same as the tap water yet, but it is OK if it is a little higher with the ammonia getting so low. Continue using a water conditioner that locks up ammonia, nitrite and nitrate so the fish are protected.

WEEK THREE

1) Clean the filter. Be very gentle, the nitrifying bacteria population is still establishing itself.

2) Continue with daily water changes, but if the pH, GH and KH are closer to the tap water then increase them to 25%.

4) Decrease the use of zeolite. Monitor the ammonia. If the plants and bacteria are handling the ammonia, then stop using zeolite. If the plants and bacteria are not up to it yet, keep using the zeolite, but perhaps only swap out the bags a couple of times this week. (The zeolite can only be rejuvenated just so many times, then is too plugged up with stuff that cannot be removed. Monitor the ammonia, and change out the zeolite bags, but remember there are other things removing the ammonia, too. It might be that the zeolite is dead, and it is time to throw it away)

By the end of week three the aquarium is likely getting back into shape. pH is much closer to the tap water pH (and KH and GH are matching the tap, too). Nitrifying bacteria and plants ought to be handling all or almost all the ammonia. You might be seeing nitrite. If nitrite shows then add 1 teaspoon of salt per 20 gallons of water. Nitrate may still be too high, (though a lot lower than 3 weeks ago). The nitrifying bacteria will be creating more nitrate as they establish themselves. Plants will be very helpful here by removing ammonia before it even gets to the bacteria.

FOURTH WEEK:

If the pH, KH and GH of tap and tank match then do as large a gravel vac and water changes as needed to really get the nitrates down.
Goal: Ammonia and Nitrite will ultimately read 0 ppm, but if the tank is still cycling try to keep the ammonia < .25 ppm, and the nitrite under 1 ppm.
Try to get and keep the nitrate under 20 ppm. Lower is better.

If the tap water pH, GH and KH are not close enough to the tank to permit larger water changes then do more frequent ones, perhaps 30% daily. It is also a good idea to keep up the deep gravel vacs to continue removing debris.

Eliminate zeolite. (Now that the bacteria is getting back to where it should be you do not need this emergency removal product, the bacteria are doing the work.)

Offer the fish a little more food if they really need it, but people who allow a tank to reach this condition are often over feeding anyway. Perhaps the new diet really is better. If your fish do need a higher protein diet, more bugs, worms, shrimp and other meaty foods add these back slowly and monitor the ammonia, nitrite and nitrate levels.

ONGOING MAINTENANCE:

Set up a schedule of weekly water changes. This might be 25% once or twice a week. If the tap water and the tank water have similar water chemistry then you can do larger water changes. Clean the filter regularly. Vacuum the floor of the tank.
Feed the fish a varied diet, making sure they eat all the food. Fast them one day per week.
Test the water weekly. Optimum readings are:
Ammonia 0 ppm. Any other result is an emergency.
Nitrite 0 ppm. Any other result is an emergency.
Nitrate < 20 ppm. If it gets higher than this you will need to do more frequent or larger water changes.
GH, KH and pH ought to be stable, not changing from week to week.
Top off with Distilled or Reverse Osmosis water.